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Catalog
ASAP is committed to accelerating the pace of discovery and informing a path to a cure for Parkinson’s disease through collaboration, research-enabling resources, and data sharing. We’ve created this catalog to showcase the research outputs and tools developed by ASAP-funded programs.
Protocol
Colonic migrating motor complexes
Protocol for ex vivo assay of colonic migrating motor complexes (CMMCs) in mouse colons.
Article
Peripheral neuronal activation shapes the microbiome and alters gut physiology
Published: The enteric nervous system shapes the intestinal environment and communicates with various brain organs, including the brain. The authors used recombinant adeno-associated viral (rAAV) vectors and chemogenetics to map and activate enteric neurons in mice with spatial and temporal resolution. View original preprint.
Protocol
3′ mRNA-sequencing
Protocol for 3′ mRNA sequencing of mouse gastrointestinal tract tissues.
Protocol
Whole gut transit time, fecal water content, and fecal output
Protocol for mouse gastrointestinal function assays (whole gut transit time, fecal water content, and fecal output).
Protocol
Metagenome preparation and analysis
Protocol for metagenomic analysis from mouse fecal pellets.
Protocol
GCaMP6f fluorescence in ex vivo intestinal preparation
Protocol for GCaMP6f imaging in ex vivo mouse intestinal tissue.
Protocol
Tissue preparation, immunohistochemistry, imaging, and quantification
Protocol for neuronal imaging.
Protocol
Virus production and administration
Protocol for AAV production and administration to mice.
Protocol
Neural activation of the GI tract
Protocol for neuronal activation of the enteric nervous system.
Code
Code for integrated multi-cohort analysis of the Parkinson’s disease gut metagenome
Detailed scripts to reproduce all analysis and data visualization for the paper, “Integrated multi-cohort analysis of the Parkinson’s disease gut metagenome,” including an interactive shiny R app for exploration of metagenomic features of interest in the data sets.
Article
Integrated multi-cohort analysis of the Parkinson’s disease gut metagenome
Preprint: Here, the fecal metagenomes of those living with PD compared to others in the household were profiled from 4 geographically-distinct sites across 3 continents. The question was whether there were any specific PD-associated signatures in gut microbiome that are either enriched or depleted in PD.
Protocol
Metabolomics preparation and analysis
Protocol for metabolomic analysis from mouse fecal and cecal samples.
Dataset
Fecal metagenomic sequencing data for PD patients and controls from the BioCollective
Fecal metagenomic sequencing data associated with Boktor et al., 2023. This dataset includes samples from the BioCollective cohort.
Dataset
Datasets associated with “Peripheral Neuronal Activation Shapes the Microbiome and Alters Gut Physiology”
This RNA data set corresponds to the preprint: Neuronal Activation of the Gastrointestinal Tract Shapes the Gut Environment in Mice (Yoo et al., 2021).